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Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte- sized Images



Peter Bajcsy, Sowon Joy Yoon, Stephen Florczyk, Nathan Hotaling, Mylene H. Simon, Piotr Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr., Mary C. Brady, Ram D. Sriram


Background: Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and spun coat, large microfiber, and medium microfiber scaffolds. Our analysis of the acquired terabyte-sized collection is motivated by the need to understand dimensionality of cell-scaffold interactions relevant to tissue engineers that grow cells on biomaterial scaffolds. Results: We designed eight contact models and down-selected them to one statistical and one geometrical model per scaffold type for visual verification based on validation experiments. A planar model for the spun coat scaffold type was validated by fitting a plane to atomic force microscopy (AFM) images with an average accuracy of R^2=0.988± 0.006 . A cylindrical model for fiber scaffolds was validated from multi-view 2D SEM images. The fiber scaffold segmentation accuracy was assessed by comparing fiber diameters from scanning electron microscopy (SEM) and confocal microscopy to be between 0.46% to 3.8% of the SEM reference values. For verification, we constructed a web-based visual verification system with 414 pairs of images with cells and their segmentation results, and with 4,968 movies with animated cell, scaffold, and contact overlays. Based on visual verification by three experts, we report the accuracy of cell segmentation to be 96.4% with 94.3% precision, and the accuracy of cell-scaffold contact for a statistical model to be 62.6% with 76.7% precision and for a geometrical model to be 93.5% with 87.6% precision. Conclusions: The novelty of our approach lies in (1) modeling cell-scaffold contact sites with statistical intensity and geometrical shape assumptions, (2) designing a methodology for validating 3D geometrical contact models, and (3) devising a mechanism for practical visual verification of hundreds of 3D measurements.
BMC Bioinformatics


Co-localization, Cellular Measurements, Cell-scaffold Contact, Segmentation Models, Contact Evaluation, Web-based Verification, Large-volume 3D Image Processing


Bajcsy, P. , , S. , Florczyk, S. , Hotaling, N. , Simon, M. , Szczypinski, P. , Schaub, N. , Simon, C. , Brady, M. and Sriram, R. (2017), Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte- sized Images, BMC Bioinformatics, [online], (Accessed April 14, 2024)
Created December 1, 2017, Updated November 10, 2018